Targets predicted by the Ago2-HITS-CLIP model are in agreement with measured fold changes after Ago2 knockdown. Analysis of predicted Ago2 binding events to 3′ UTRs that are upregulated after Ago2 knockdown at day 2 for transcripts falling into the following fold-change categories: downregulated (fold change below 0.7, 804 UTRs), unchanged (fold change between 0.7 and 1.4, 6,893 UTRs), weakly upregulated (fold change between 1.4 and 2.0, 713 UTRs) and strongly upregulated (fold change greater than 2.0, 136 UTRs). (A) Fraction of 3′ UTRs with at least one Ago2 binding site hit. Asterisks indicate a statistically significant increase (t-test: * P<0.05; ** P<0.001). (B) Number of binding site hits per 3′ UTR. Asterisks indicate a statistically significant increase (Wilcoxon rank sum test: * P<0.05; ** P<0.001). Box plots do not include outliers, for that reason we show the full distributions in Additional file 4. HITS-CLIP, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation; UTR, untranslated region.